Don't Worry.
I did my MSc in the UK while working full time in the UAE. And my eligibility passed just fine. As long as you have payslips and the reference letter, you're good to go.
But Note : The nature of my job requires traveling and is not really office based. So, I had my travel history and the reference letter to back that up. In my GCMS notes however there were no problems. Not even a mention that this is a conflict or anything. My theory is that as long as you're doing that outside Canada, you're fine.